Protecting groups for “Z nucleotide” and methods thereof

An oligonucleotide, wherein at least one of the nucleotides has the structural formula of:

• wherein
• R1 is an electron withdrawing group;
• A is O or S;
• R2 is OR2′ and R2′ is 1,1-dioxo-thiomorpholine-4-carbothioate (TC), tert-butyldimethylsilyl (TBDMS), tri-iso-propylsilyloxymethyl (TOM), bis(2-acetoxyethoxy)methyl (ACE), pivaloyloxymethyl (PivOM), 1-(2-cyanoethoxy)ethyl (CEE), 2-cyanoethoxymethyl (CEM), —CO—R″, —CH2—CH═CH2, —CH2—O—CH2-phenyl-NO2, —CH2—O—CH2—CH2—SO2-aryl, or —Si(R″)3, wherein R″ is independently selected from straight-, branched-, saturated or unsaturated-alkyl, aryl, alkaryl, and aralkyl;
• R is a protected amino group of the formula N═C(R′)NR′2 or N(R′)COR′ or N(COR′)2, wherein each R′ is independently selected from H, linear-, branched-, saturated- or unsaturated-alkyl, aryl, alkaryl and aralkyl;
• or wherein R is a protected amino group of the formula N═C(R′)NR′2, wherein NR′2 is joined to form a 5-8 membered ring wherein said ring can contain a heteroatom selected from O or S;
• and
• each of X, Y and Z is independently H, halogen, or a C1-C3 alkyl, wherein two or more of X, Y and Z may together form a 5-8 membered saturated, un-saturated or aryl ring.

A method for synthesizing an oligonucleotide, comprising:

• protecting an unnatural nucleotide with an acetyl-oxy-methyl group,
• incorporating the protected unnatural nucleotide into a nucleotide sequence on a solid support;
• and
• removing the acetyl-oxy-methyl group from the unnatural nucleotide incorporated into the nucleotide sequence,
• wherein the protected unnatural nucleotide has the structural formula (V),
• wherein
• R1 is an electron withdrawing group;
• A is O or S;
• R2 is OR2′ and R2′ is 1,1-dioxo-thiomorpholine-4-carbothioate (TC), tert-butyldimethylsilyl (TBDMS), tri-iso-propylsilyloxymethyl (TOM), bis(2-acetoxyethoxy)methyl (ACE), pivaloyloxymethyl (PivOM), 1-(2-cyanoethoxy)ethyl (CEE), 2-cyanoethoxymethyl (CEM), —CO—R″, —CH2—CH═CH2, —CH2—O—CH2-phenyl-NO2, —CH2—O—CH2—CH2—SO2-aryl, or —Si(R″)3, wherein R″ is independently selected from straight-, branched-, saturated or unsaturated-alkyl, aryl, alkaryl, and aralkyl;
• and
• R is a protected amino group of the formula N═C(R′)NR′2 or N(R′)COR′ or N(COR′)2, wherein each R′ is independently selected from H, linear-, branched-, saturated- or unsaturated-alkyl, aryl, alkaryl and aralkyl, or wherein R is a protected amino group of the formula N═CR′NR′2, NR′2 is joined to form a 5-8 membered ring wherein said ring can contain a heteroatom selected from O or S;
• each of X, Y and Z is independently H, halogen, or a C1-C3 alkyl, wherein two or more of X, Y and Z may together form a 5-8 membered saturated, un-saturated or aryl ring.